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CCDC12 coiled-coil domain containing 12 [ Homo sapiens (human) ]

Gene ID: 151903, updated on 17-Jun-2024

Summary

Official Symbol
CCDC12provided by HGNC
Official Full Name
coiled-coil domain containing 12provided by HGNC
Primary source
HGNC:HGNC:28332
See related
Ensembl:ENSG00000160799 AllianceGenome:HGNC:28332
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 3.1), spleen (RPKM 2.9) and 25 other tissues See more
Orthologs
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Genomic context

See CCDC12 in Genome Data Viewer
Location:
3p21.31
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46921730..46981994, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46938112..46998350, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (46963220..47023484, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46929375-46930132 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46930133-46930890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46931649-46932404 Neighboring gene myosin light chain 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14297 Neighboring gene parathyroid hormone 1 receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46950549-46951124 Neighboring gene Sharpr-MPRA regulatory region 5172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46966125-46966626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46972095-46972610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19802 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:46972611-46973126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46975255-46976022 Neighboring gene Sharpr-MPRA regulatory region 2536 Neighboring gene uncharacterized LOC124909375 Neighboring gene BLVRB pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46981287-46981788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46981789-46982288 Neighboring gene Sharpr-MPRA regulatory region 10220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47002103-47002604 Neighboring gene NANOG hESC enhancer GRCh37_chr3:47006121-47006678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47007588-47008518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47008519-47009448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47016719-47017421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47017422-47018123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:47018827-47019527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47021430-47022210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47022211-47022991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47026300-47027052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47039103-47039996 Neighboring gene neurobeachin like 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47050749-47051546 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47051547-47052343 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47054299-47054798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14303 Neighboring gene neurotrophin receptor associated death domain, pseudogene Neighboring gene SET domain containing 2, histone lysine methyltransferase Neighboring gene mitochondrial ribosomal protein L57 pseudogene 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ39430, FLJ40801, MGC23918

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
part_of U2-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
part_of post-mRNA release spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
coiled-coil domain-containing protein 12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001277074.2NP_001264003.1  coiled-coil domain-containing protein 12 isoform 2

    See identical proteins and their annotated locations for NP_001264003.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate internal promoter and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AC094020, AC109583
    Consensus CDS
    CCDS2748.3
    UniProtKB/Swiss-Prot
    Q8N8I4, Q8WUD4
    Related
    ENSP00000508011.1, ENST00000683445.1
    Conserved Domains (1) summary
    pfam08315
    Location:11143
    cwf18; cwf18 pre-mRNA splicing factor
  2. NM_144716.6NP_653317.2  coiled-coil domain-containing protein 12 isoform 1

    See identical proteins and their annotated locations for NP_653317.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC094020, AC109583
    Consensus CDS
    CCDS63612.1
    UniProtKB/TrEMBL
    A0A024R2U3, A0A9K3Y8B6, J3KR35
    Related
    ENSP00000292314.2, ENST00000292314.6
    Conserved Domains (1) summary
    pfam08315
    Location:24156
    cwf18; cwf18 pre-mRNA splicing factor

RNA

  1. NR_102269.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because it lacks a supported ORF that is likely to result in a protein product.
    Source sequence(s)
    AC094020, BM676030, BM803652, DA952452

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    46921730..46981994 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    46938112..46998350 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)